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Updated printouts to help with debugging. Issue does appear to be deterministic though. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5950 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-06 01:04:07 +00:00
parent 27dfb53d26
commit 2c57721ed2
1 changed files with 8 additions and 15 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -641,11 +641,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// if there are any known indels for this region, get them and create alternate consenses // if there are any known indels for this region, get them and create alternate consenses
generateAlternateConsensesFromKnownIndels(altConsenses, leftmostIndex, reference); generateAlternateConsensesFromKnownIndels(altConsenses, leftmostIndex, reference);
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: reads.size() = " + reads.size());
}
// decide which reads potentially need to be cleaned; // decide which reads potentially need to be cleaned;
// if there are reads with a single indel in them, add that indel to the list of alternate consenses // if there are reads with a single indel in them, add that indel to the list of alternate consenses
long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference); long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference);
@ -656,11 +651,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n"); // if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n");
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: altConsenses.size() after seeing reads = " + altConsenses.size());
}
Consensus bestConsensus = null; Consensus bestConsensus = null;
Iterator<Consensus> iter = altConsenses.iterator(); Iterator<Consensus> iter = altConsenses.iterator();
@ -872,11 +862,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
continue; continue;
} }
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: read = " + read.getReadName() + " " + read.getCigarString());
}
final AlignedRead aRead = new AlignedRead(read); final AlignedRead aRead = new AlignedRead(read);
// first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence // first, move existing indels (for 1 indel reads only) to leftmost position within identical sequence
@ -1582,6 +1567,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight); loc = getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), padLeft, padRight);
reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
StringUtil.toUpperCase(reference); StringUtil.toUpperCase(reference);
// TODO -- REMOVE ME WHEN WE FIND THE NON-DETERMINISM
if ( OUT_STATS != null ) {
logger.warn("ERIC: padLeft = " + padLeft);
logger.warn("ERIC: padRight = " + padRight);
logger.warn("ERIC: loc = " + loc);
logger.warn("ERIC: reference = " + new String(reference));
}
} }
return reference; return reference;